file_tag = sprintf("%s_BL_%s", cell_type_name, graph_weight)
assayed_genes = scan(sprintf("output/gene_list_%s.txt", file_tag),
what = character(), sep="\n")
gene_sets = scan(sprintf("output/name_s_%s.txt", file_tag),
what = character(), sep="\n")
gene_sets = sapply(gene_sets, strsplit, USE.NAMES=FALSE, split=",")
n_genes = sapply(gene_sets, length)
names(n_genes) = NULL
summary(n_genes)## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 16.00 20.00 20.00 20.18 21.00 22.00
## [1] 40
## [1] 16 18 19 19 19 19 19 19 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20
## [26] 20 21 21 21 21 21 21 21 21 21 22 22 22 22 22
bioMart.All the gene symbols that can be found in bioMart are
consistent with what we have. So no need to run it.
ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
gene_BM = getBM(attributes = c("hgnc_symbol", "external_gene_name"),
filters = "external_gene_name",
values = assayed_genes,
mart = ensembl)
length(assayed_genes)
dim(gene_BM)
gene_BM[1:2,]
table(assayed_genes %in% gene_BM$external_gene_name)
t1 = table(gene_BM$external_gene_name)
dup = names(t1)[t1 > 1]
gene_BM[gene_BM$external_gene_name %in% dup,]
table(gene_BM$hgnc_symbol == gene_BM$external_gene_name)
w2kp = which(gene_BM$hgnc_symbol != gene_BM$external_gene_name)
gene_BM[w2kp,]alias2Symbol function from
limma.a2s = rep(NA, length(assayed_genes))
for(i in 1:length(assayed_genes)){
gi = assayed_genes[i]
ai = alias2Symbol(gi)
if(length(ai) > 1){
print(gi)
print(ai)
}
a2s[i] = ai[1]
}## [1] "HIST1H2BC"
## [1] "H2BC5" "H2BC4"
## [1] "MPP6"
## [1] "MPHOSPH6" "PALS2"
## [1] "MARS"
## [1] "MARS1" "SLA2"
## [1] "SEPT2"
## [1] "SEPTIN6" "SEPTIN2"
##
## FALSE TRUE
## 1951 49
##
## FALSE TRUE <NA>
## 45 1906 49
gene_info = data.table(sym_in_data = assayed_genes, sym_limma = a2s)
gene_info[sym_in_data != sym_limma,]## sym_in_data sym_limma
## 1: ADPRHL2 ADPRS
## 2: AES TLE5
## 3: C12orf45 NOPCHAP1
## 4: C3orf58 DIPK2A
## 5: C6orf99 LINC02901
## 6: CBWD2 ZNG1B
## 7: CXorf57 RADX
## 8: FAM102A EEIG1
## 9: FAM122C PABIR3
## 10: FAM153C FAM153CP
## 11: FAM160A2 FHIP1B
## 12: GRASP TAMALIN
## 13: H2AFX H2AX
## 14: HIST1H2AG H2AC11
## 15: HIST1H2BC H2BC5
## 16: HIST1H2BK H2BC12
## 17: HIST1H2BN H2BC15
## 18: HIST1H3A H3C1
## 19: HIST1H3H H3C10
## 20: HIST1H4C H4C3
## 21: HIST2H2BF H2BC18
## 22: LRMP IRAG2
## 23: MFSD14C MFSD14CP
## 24: MKL1 MRTFA
## 25: MPP6 MPHOSPH6
## 26: RNASEH1-AS1 RNASEH1-DT
## 27: SEPT6 SEPTIN6
## 28: SEPT9 SEPTIN9
## 29: TMEM161B-AS1 TMEM161B-DT
## 30: ARNTL BMAL1
## 31: C6orf106 ILRUN
## 32: C6orf203 MTRES1
## 33: FAM129A NIBAN1
## 34: FAM160B1 FHIP2A
## 35: FAM192A PSME3IP1
## 36: HEXDC HEXD
## 37: HIST1H1E H1-4
## 38: KIAA0100 BLTP2
## 39: KIAA1551 RESF1
## 40: LARS LARS1
## 41: MARS MARS1
## 42: PLA2G16 PLAAT3
## 43: SEPT2 SEPTIN6
## 44: SMIM37 MTLN
## 45: YARS YARS1
## sym_in_data sym_limma
gene_info[, gene_symbol := sym_in_data]
gene_info[which(sym_in_data != sym_limma), gene_symbol := sym_limma]
dim(gene_info)## [1] 2000 3
## sym_in_data sym_limma gene_symbol
## 1: ABCD3 ABCD3 ABCD3
## 2: ABCG1 ABCG1 ABCG1
## 3: ABHD5 ABHD5 ABHD5
## 4: ABI1 ABI1 ABI1
## 5: ABLIM1 ABLIM1 ABLIM1
## t1
## 1 2
## 1998 1
## sym_in_data sym_limma gene_symbol
## 1: SEPT6 SEPTIN6 SEPTIN6
## 2: SEPT2 SEPTIN6 SEPTIN6
Gene set annotations (by gene symbols) were downloaded from MSigDB website.
gmtfile = list()
gmtfile[["reactome"]] = "../Annotation/c2.cp.reactome.v2023.2.Hs.symbols.gmt"
gmtfile[["go_bp"]] = "../Annotation/c5.go.bp.v2023.2.Hs.symbols.gmt"
gmtfile[["immune"]] = "../Annotation/c7.all.v2023.2.Hs.symbols.gmt"
pathways = list()
for(k1 in names(gmtfile)){
pathways[[k1]] = gmtPathways(gmtfile[[k1]])
}
names(pathways)## [1] "reactome" "go_bp" "immune"
## reactome go_bp immune
## 1692 7647 5219
Filter gene sets for size between 10 and 500.
## $reactome
## 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
## 5.0 7.0 9.0 12.0 17.0 23.0 31.0 44.0 71.8 120.9 1463.0
##
## $go_bp
## 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
## 5.0 6.0 8.0 10.0 14.0 19.0 29.0 46.0 80.8 183.0 1966.0
##
## $immune
## 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
## 5 162 193 197 199 199 200 200 200 200 1992
## [1] 2000 3
max_n2kp = 10
goseq_res = NULL
for(k in 1:length(gene_sets)){
if(length(gene_sets[[k]]) < 10) { next }
print(k)
set_k = paste0("set_", k)
print(gene_sets[[k]])
genes = gene_info$sym_in_data %in% gene_sets[[k]]
names(genes) = gene_info$gene_symbol
table(genes)
pwf = nullp(genes, "hg38", "geneSymbol")
for(k1 in names(pathways)){
p1 = pathways[[k1]]
res1 = goseq(pwf, "hg38", "geneSymbol",
gene2cat=goseq:::reversemapping(p1))
res1$FDR = p.adjust(res1$over_represented_pvalue, method="BH")
nD = sum(res1$FDR < 0.1)
if(nD > 0){
res1 = res1[order(res1$FDR),][1:min(nD, max_n2kp),]
res1$category = gsub("REACTOME_|GOBP_", "", res1$category)
res1$category = gsub("_", " ", res1$category)
res1$category = tolower(res1$category)
res1$category = substr(res1$category, start=1, stop=81)
goseq_res[[set_k]][[k1]] = res1
}
}
}## [1] 1
## [1] "CHD2" "ENOSF1" "GRASP" "JPX" "PHYH" "TBCCD1"
## [7] "TCTA" "YPEL2" "ZNF831" "ABHD2" "ERICH1" "GNPAT"
## [13] "IRAK4" "MORC3" "NLRC5" "ODF3B" "PEX11B" "SEC14L1"
## [19] "TNFRSF18" "ZBP1" "ZNF236"
## [1] 2
## [1] "ARHGAP9" "ARID4A" "CCM2" "CD96" "CITED2" "DGKA"
## [7] "HELQ" "HIST1H3H" "IFRD1" "ING2" "MXD1" "RCAN3"
## [13] "RGCC" "RIC1" "SLC12A7" "SLC8B1" "STARD10" "TESPA1"
## [19] "TMEM204" "WARS2"
## [1] 3
## [1] "AC093323.1" "AC245297.3" "ERVK3-1" "FAM122C" "GPCPD1"
## [6] "LINC01215" "LINC02265" "MAP3K2" "MDS2" "PLCL1"
## [11] "SLC25A32" "ST7L" "TBPL1" "TRAV38-2DV8" "TRBV5-4"
## [16] "TRBV6-6" "TRBV7-3" "TTC3" "ZNF506" "MIR4435-2HG"
## [21] "PMVK"
## [1] 4
## [1] "AC007952.4" "AC025164.1" "AC087239.1" "ATP2B1-AS1" "CD82"
## [6] "CSKMT" "IER2" "ILF3-DT" "LBH" "LINC00861"
## [11] "NPIPB4" "NUP58" "PPP1R15A" "PRR7" "SLC2A3"
## [16] "TAGAP" "WHAMM" "Z93241.1" "AZI2" "CCDC43"
## [21] "ITGAL" "N4BP1"
## [1] 5
## [1] "CCDC66" "CDC42SE2" "CEP95" "EPHB6" "FHIT" "FOXN3"
## [7] "HIST1H2BC" "NR4A3" "NSUN6" "PIK3IP1" "PLK3" "RSRP1"
## [13] "SENP7" "SLC44A1" "WSB1" "ZFP36L1" "ITK" "RECK"
## [19] "SAMD9"
## [1] 6
## [1] "ABHD5" "AC119396.1" "AC245014.3" "AL133415.1" "AL139246.5"
## [6] "ARL4A" "ATG9B" "FBXO3" "IL23A" "LTB"
## [11] "MCUB" "MHENCR" "NAA16" "NOP53" "POLD4"
## [16] "SCML4" "SLC25A38" "SNRK" "TBCC" "TNFRSF25"
## [21] "ZC3H12D"
## [1] 7
## [1] "COQ7" "IER3" "MZF1" "ADGRE5" "ARL4C" "C1orf21" "CFD"
## [8] "CST7" "CX3CR1" "DIAPH2" "ETNK1" "GZMM" "MCTP2" "NCBP3"
## [15] "PLEK" "PPP2R5B" "PTGDR" "PTPN7" "RNPEPL1" "TTC16"
## [1] 8
## [1] "AC008105.3" "AC025171.2" "ADA2" "AK5" "ARRDC2"
## [6] "CHRM3-AS2" "DNASE1" "GSTM4" "KLF7" "NRIP1"
## [11] "NUAK2" "PDE7A" "RNASEH1-AS1" "SLC22A17" "TUBD1"
## [16] "TUBE1" "ZNF84" "ZNF862" "SPTLC2" "TMEM62"
## [1] 9
## [1] "ANKH" "CSRNP1" "DHRS3" "EPHX2" "KANSL2" "OXLD1"
## [7] "PECAM1" "ZNF10" "C12orf75" "GON4L" "IL4R" "INPP5D"
## [13] "KMT2B" "NARF" "PHF20" "PHF20L1" "SP140" "TNFRSF4"
## [1] 10
## [1] "MFSD14C" "STARD7" "WAPL" "ABHD3" "AC016831.7"
## [6] "AC022916.1" "AC118549.1" "CARMIL2" "EAPP" "ECPAS"
## [11] "KANSL1-AS1" "NRDC" "PARP11" "PUM3" "RAPGEF1"
## [16] "SLC20A2" "SPATA13" "TM2D1" "UTP25" "Z93930.2"
## [1] 11
## [1] "BCL3" "C20orf204" "DDX3Y" "EIF1AY" "FAAH2" "HRH2"
## [7] "KDM5D" "OSM" "PCSK1N" "RPS4Y1" "S100A12" "SLF2"
## [13] "SOCS3" "TTTY15" "UTY" "ZFYVE28"
## [1] 12
## [1] "AC145124.1" "AIF1" "AKIRIN1" "BOLA2-SMG1P6" "C12orf45"
## [6] "COQ10B" "CRLF3" "IL16" "LINC01550" "MMP28"
## [11] "MYNN" "NUDT4" "OSER1" "OTULINL" "PECR"
## [16] "TMEM161B-AS1" "TMEM71" "YY1AP1" "JAKMIP1" "SERTAD3"
## [21] "SUSD6" "TMEM138"
## [1] 13
## [1] "DELE1" "DSE" "GIMAP1" "IER5" "KLRB1" "PITPNC1"
## [7] "RAB37" "SLC25A33" "SNX18" "TBC1D10C" "TRBC2" "TTC31"
## [13] "UCP2" "APOBEC3G" "GNPTAB" "GZMB" "KLRG1" "LAG3"
## [19] "MATK" "SMPD2"
## [1] 14
## [1] "ERCC5" "FAM8A1" "BROX" "CCDC88B" "CD320" "CISH" "CTBS"
## [8] "FKBP11" "IL2RB" "IL2RG" "KCNAB2" "PRDM1" "PREP" "PVT1"
## [15] "REXO2" "RNMT" "STAT4" "TGS1" "TSHZ2" "UGCG"
## [1] 15
## [1] "AC084033.3" "AMD1" "CAMK4" "CCDC141" "CXorf57"
## [6] "EVI2B" "FAM102A" "FAM117B" "FYB1" "INPP4B"
## [11] "IPCEF1" "MAML2" "MTRNR2L12" "SNHG12" "TC2N"
## [16] "TMC8" "TMEM107" "TSC22D2" "ADAM19" "SCAMP4"
## [21] "ZNF292"
## [1] 16
## [1] "ATAD1" "BTN3A1" "CHMP1B" "CHMP7" "COG5" "DBP"
## [7] "DIP2B" "LRRC8D" "NSMAF" "PARP16" "PCNP" "PPP1R15B"
## [13] "SPIDR" "STX16" "THAP6" "TMEM245" "TSPYL4" "ZBTB25"
## [19] "ZMAT1" "BTN3A2" "NEK9" "TAOK3"
## [1] 17
## [1] "AC016405.3" "AC020911.2" "AC025171.3" "AC091271.1" "AC103591.3"
## [6] "AF213884.3" "AL121944.1" "AL357060.1" "AL451085.1" "C6orf99"
## [11] "ID3" "JAML" "KLF12" "LINC01465" "LRRN3"
## [16] "OSER1-DT" "PARP8" "PNISR" "CNOT4" "SDF2"
## [21] "WDR7"
## [1] 18
## [1] "AL627171.1" "NDUFV2-AS1" "ZNF490" "ADTRP" "ATAD2B"
## [6] "CEMIP2" "CRYBG1" "GRK2" "IGLV3-25" "KIAA0040"
## [11] "LRRC58" "MT1X" "NORAD" "SLFN12L" "SNHG9"
## [16] "TENT5C" "THUMPD3-AS1" "TRBV6-1" "UBALD2" "VPS13D"
## [1] 19
## [1] "CLK4" "MYADM" "ZNF821" "BLOC1S6" "C2orf68" "CD7" "CLASRP"
## [8] "IFNAR1" "KLF9" "NME3" "P4HTM" "PIK3CB" "PIM2" "PRMT2"
## [15] "RNF145" "SACS" "SETD5" "SLC35A2" "SNX9" "SP140L"
## [1] 20
## [1] "AC025159.1" "AL135791.1" "CERNA1" "LDLRAP1" "LINC02273"
## [6] "LRRC8C-DT" "LYRM9" "NSMCE3" "PITPNA-AS1" "SNHG7"
## [11] "TSPOAP1-AS1" "AC020915.3" "GPR132" "HACD3" "MFSD14A"
## [16] "NNT-AS1" "NSD3" "TOMM70" "TSPAN14" "TUT4"
## [1] 21
## [1] "ADK" "ARL6IP1" "C6orf62" "EFCAB2" "HEATR5B" "MBD6" "MTERF4"
## [8] "ST3GAL1" "STMN3" "TOB2" "TPP2" "EHMT1" "FRY" "FRYL"
## [15] "ICE1" "SDR39U1" "SYNRG" "UBA7" "UBE3B" "VPS36"
## [1] 22
## [1] "CBLL1" "CST3" "FAM118A" "FCN1" "GIMAP8" "IGKV1-5"
## [7] "IGLV1-44" "NT5DC1" "PYROXD1" "RABL2B" "ALOX5AP" "GAB3"
## [13] "IFI44" "KIAA1551" "MX2" "OAS2" "PPP2R3C" "SRP54"
## [19] "STK10"
## [1] 23
## [1] "RBKS" "SUPT20H" "AC116407.2" "APOL6" "ARHGEF3"
## [6] "ATXN7L3B" "C4orf48" "CARD16" "ENY2" "GIMAP7"
## [11] "LPIN1" "LPIN2" "MESD" "PDE4B" "PHPT1"
## [16] "PTGER2" "RCBTB2" "RNF19A" "TCAF2" "TMEM156"
## [1] 24
## [1] "AL118516.1" "KIF9" "RGS10" "UPF3A" "BUD23"
## [6] "CD69" "CYTIP" "DDIT4" "EFR3A" "GIMAP4"
## [11] "IFITM2" "ISG20" "KLF6" "MTRNR2L8" "NAA38"
## [16] "NADSYN1" "NBDY" "SIGIRR" "SMIM37" "STK17B"
## [1] 25
## [1] "CD38" "IGLV2-14" "KIAA1328" "MBNL2" "RPS26" "SIMC1"
## [7] "XIST" "APOL1" "CCL5" "CCR4" "GZMA" "LINC01871"
## [13] "MYO1G" "RAP1GAP2" "RSAD2" "SAMD9L" "SPON2" "TGFBR3"
## [19] "VCAN"
## [1] 26
## [1] "NFYB" "PHC1" "ANK3" "ARID5B" "CCDC12" "CREBZF" "GCN1"
## [8] "IL32" "NFE2L1" "NQO2" "NT5C" "PCGF5" "PLAC8" "SYTL1"
## [15] "TIPARP" "TMED4" "XBP1" "ZDHHC20" "ZNF593"
## [1] 27
## [1] "AC009061.2" "AL645728.1" "AP002360.1" "C12orf29" "COX10"
## [6] "FBXO8" "GIMAP6" "HDHD2" "IL6R" "KLHL6"
## [11] "LST1" "MAST4" "NBPF14" "OTUD5" "RETREG1"
## [16] "SMDT1" "TBCK" "TRAV8-6" "ZFP14" "BISPR"
## [21] "C12orf4" "PARP4"
## [1] 28
## [1] "CD28" "KLF10" "ODC1" "SH3YL1" "AGAP2" "AP3M2" "AREG"
## [8] "CRIP2" "CRTC3" "EDA" "GABPB2" "ICOS" "IL21R" "KHNYN"
## [15] "LTBP3" "LY96" "NFKBIZ" "PLEKHA2" "SMAD5" "TOB1" "ZNF101"
## [1] 29
## [1] "C16orf74" "C1GALT1" "COQ8A" "CTSF" "FCMR" "HIVEP2"
## [7] "LEPROT" "LIMD2" "LIPT1" "MLXIP" "ORC4" "PCMTD2"
## [13] "RASA2" "SPART" "TBC1D7" "TMEM154" "TRABD2A" "TRAV23DV6"
## [19] "ZNF140" "NDUFC1" "TMEM175"
## [1] 30
## [1] "DPEP2" "FAM227B" "GGT7" "MAP3K8" "ZFX" "ASCL2" "B3GALT4"
## [8] "CCDC112" "CD58" "FAM129A" "GALNS" "IFIT1" "IFIT2" "IFIT3"
## [15] "NBEAL2" "NRROS" "PHF23" "POGLUT1" "ZEB2" "ZNF276"
## [1] 31
## [1] "RNASEK" "ARHGAP10" "BCL9L" "CARD11" "CMIP" "CROT"
## [7] "DENND4B" "EIF2AK4" "GPRIN3" "IFI35" "KIF21A" "KIF21B"
## [13] "KLHDC4" "LY6E" "PLA2G16" "PRDM2" "PREX1" "SBNO2"
## [19] "SCAF8" "SLA"
## [1] 32
## [1] "AC004687.1" "AC027644.3" "AC097376.2" "AL359220.1" "CASP4"
## [6] "COQ10A" "GOLGA8B" "GZMK" "KCNK6" "MATR3-1"
## [11] "MUC20-OT1" "RGS1" "TRAV12-2" "TRAV25" "TRAV41"
## [16] "TRBV6-5" "WASHC4" "ZNF600" "ZNF91" "FRMD4B"
## [21] "SPOCK2"
## [1] 33
## [1] "ACADSB" "C3orf58" "COL18A1" "DAPP1" "FAM153C" "INTS6"
## [7] "IP6K2" "MYLIP" "NABP1" "NEK1" "NR1D1" "NR1D2"
## [13] "PLEKHM1" "RCSD1" "SLC26A11" "TECPR1" "DOCK11" "LPCAT4"
## [19] "PPRC1"
## [1] 34
## [1] "BTG1" "BTG2" "C1orf43" "EGR1" "FBXL3" "LCLAT1" "TCF7"
## [8] "ATP8B2" "CHD6" "ETV6" "FBXO9" "IFNGR2" "KIF3B" "NEAT1"
## [15] "PCED1B" "PIEZO1" "RHOH" "TBC1D14" "ZNF708"
## [1] 35
## [1] "ODF2L" "UTP6" "YPEL5" "ANKAR" "DTX3L" "FAM53B" "GBP1" "GBP3"
## [9] "GBP5" "GNLY" "HSH2D" "IFI44L" "IRF1" "IRF9" "MX1" "MYO1F"
## [17] "NKG7" "PARP14" "PARP9" "XAF1"
## [1] 36
## [1] "AC013264.1" "ACSS1" "AL138963.3" "ANXA2R" "C7orf31"
## [6] "CFAP36" "LINC00623" "METAP1" "METTL21A" "SNHG8"
## [11] "SP3" "STK19" "TRAV12-1" "TRAV13-2" "TRAV21"
## [16] "TRAV8-3" "TRAV9-2" "TRBV28" "TRBV6-2" "ZFAS1"
## [21] "ZNF749" "C1orf162"
## [1] 37
## [1] "ARHGAP15" "ATG13" "CD40LG" "DPYD" "ERAP2" "HOXB2"
## [7] "IGKV3-20" "LAX1" "SGSM3" "SLC7A6" "TCP11L2" "TGIF1"
## [13] "TRAV14DV4" "TRBC1" "TTC39C" "UBL3" "XRRA1" "CARD8-AS1"
## [19] "MT2A" "OAS1"
## [1] 38
## [1] "AC004854.2" "AC015982.1" "AC023157.3" "AC083880.1" "AC087623.3"
## [6] "ARF4-AS1" "BX284668.6" "HIPK1-AS1" "JCHAIN" "KCNQ1OT1"
## [11] "LETM2" "LINC00649" "MZF1-AS1" "NOCT" "NPIPB11"
## [16] "NPIPB5" "PHLDA1" "SDR42E2" "THAP9-AS1" "TOX"
## [21] "MYBL1"
## [1] 39
## [1] "ABCC10" "ADGRG1" "AKNA" "CCL4" "CD300A" "CTSW"
## [7] "FCRL6" "FGFBP2" "GPR65" "MIAT" "PAXX" "RASAL3"
## [13] "S1PR5" "TRANK1" "TRAV29DV5" "TRBV12-3" "TSPAN32" "TTC38"
## [19] "USP30-AS1" "ZNF683"
## [1] 40
## [1] "ARMH1" "COA1" "LRMP" "RAB33B" "RNF139" "TRAV8-2"
## [7] "ZSCAN18" "APH1B" "CITED4" "COL6A3" "COX17" "HELB"
## [13] "RNF157" "RTKN2" "SESN3" "SLC23A2" "SLC25A37" "SLC9A8"
## [19] "TAF4B" "ZNF267"
for(n1 in names(goseq_res)){
k = as.numeric(gsub("set_", "", n1))
print(n1)
print(gene_sets[[k]])
print(goseq_res[[n1]])
}## [1] "set_7"
## [1] "COQ7" "IER3" "MZF1" "ADGRE5" "ARL4C" "C1orf21" "CFD"
## [8] "CST7" "CX3CR1" "DIAPH2" "ETNK1" "GZMM" "MCTP2" "NCBP3"
## [15] "PLEK" "PPP2R5B" "PTGDR" "PTPN7" "RNPEPL1" "TTC16"
## $immune
## category
## 717 gse15735 ctrl vs hdac inhibitor treated cd4 tcell 2h dn
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 717 1.526635e-05 0.9999994 5 33
## FDR
## 717 0.07795
##
## [1] "set_9"
## [1] "ANKH" "CSRNP1" "DHRS3" "EPHX2" "KANSL2" "OXLD1"
## [7] "PECAM1" "ZNF10" "C12orf75" "GON4L" "IL4R" "INPP5D"
## [13] "KMT2B" "NARF" "PHF20" "PHF20L1" "SP140" "TNFRSF4"
## $reactome
## category
## 352 formation of wdr5 containing histone modifying complexes
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 352 4.450854e-06 0.9999999 4 16
## FDR
## 352 0.005345475
##
## $go_bp
## category over_represented_pvalue
## 1112 histone h3 k4 methylation 1.374380e-05
## 1115 histone modification 3.378768e-05
## 1114 histone methylation 3.485187e-05
## 2369 peptidyl lysine methylation 6.151068e-05
## 1113 histone h4 acetylation 6.798180e-05
## 1211 internal protein amino acid acetylation 7.137034e-05
## 2370 peptidyl lysine modification 7.611393e-05
## 2367 peptidyl lysine acetylation 1.044145e-04
## 3147 protein methylation 1.278195e-04
## under_represented_pvalue numDEInCat numInCat FDR
## 1112 0.9999999 3 8 0.05200756
## 1115 0.9999992 4 29 0.05200756
## 1114 0.9999997 3 10 0.05200756
## 2369 0.9999992 3 12 0.05200756
## 1113 1.0000000 2 2 0.05200756
## 1211 0.9999991 3 12 0.05200756
## 2370 0.9999977 4 36 0.05200756
## 2367 0.9999984 3 14 0.06242683
## 3147 0.9999979 3 15 0.06792894
##
## [1] "set_11"
## [1] "BCL3" "C20orf204" "DDX3Y" "EIF1AY" "FAAH2" "HRH2"
## [7] "KDM5D" "OSM" "PCSK1N" "RPS4Y1" "S100A12" "SLF2"
## [13] "SOCS3" "TTTY15" "UTY" "ZFYVE28"
## $immune
## category
## 4353 gse5099 classical m1 vs alternative m2 macrophage dn
## 3753 gse39820 ctrl vs il1b il6 cd4 tcell dn
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 4353 1.764486e-05 0.9999996 4 21
## 3753 2.103421e-05 0.9999992 5 48
## FDR
## 4353 0.05370035
## 3753 0.05370035
##
## [1] "set_13"
## [1] "DELE1" "DSE" "GIMAP1" "IER5" "KLRB1" "PITPNC1"
## [7] "RAB37" "SLC25A33" "SNX18" "TBC1D10C" "TRBC2" "TTC31"
## [13] "UCP2" "APOBEC3G" "GNPTAB" "GZMB" "KLRG1" "LAG3"
## [19] "MATK" "SMPD2"
## $immune
## category over_represented_pvalue
## 4253 gse45739 unstim vs acd3 acd28 stim wt cd4 tcell dn 1.584655e-05
## under_represented_pvalue numDEInCat numInCat FDR
## 4253 0.9999991 6 61 0.08091246
##
## [1] "set_22"
## [1] "CBLL1" "CST3" "FAM118A" "FCN1" "GIMAP8" "IGKV1-5"
## [7] "IGLV1-44" "NT5DC1" "PYROXD1" "RABL2B" "ALOX5AP" "GAB3"
## [13] "IFI44" "KIAA1551" "MX2" "OAS2" "PPP2R3C" "SRP54"
## [19] "STK10"
## $reactome
## category over_represented_pvalue
## 187 creation of c4 and c2 activators 1.256826e-05
## 460 initial triggering of complement 3.204746e-05
## 171 complement cascade 6.474635e-05
## under_represented_pvalue numDEInCat numInCat FDR
## 187 0.9999999 3 6 0.01509448
## 460 0.9999997 3 8 0.01924450
## 171 0.9999992 3 10 0.02592012
##
## [1] "set_23"
## [1] "RBKS" "SUPT20H" "AC116407.2" "APOL6" "ARHGEF3"
## [6] "ATXN7L3B" "C4orf48" "CARD16" "ENY2" "GIMAP7"
## [11] "LPIN1" "LPIN2" "MESD" "PDE4B" "PHPT1"
## [16] "PTGER2" "RCBTB2" "RNF19A" "TCAF2" "TMEM156"
## $reactome
## category over_represented_pvalue under_represented_pvalue
## 1170 triglyceride biosynthesis 5.64769e-05 1.0000000
## 1073 synthesis of pe 1.42343e-04 0.9999997
## numDEInCat numInCat FDR
## 1170 2 2 0.06782876
## 1073 2 3 0.08547700
##
## [1] "set_24"
## [1] "AL118516.1" "KIF9" "RGS10" "UPF3A" "BUD23"
## [6] "CD69" "CYTIP" "DDIT4" "EFR3A" "GIMAP4"
## [11] "IFITM2" "ISG20" "KLF6" "MTRNR2L8" "NAA38"
## [16] "NADSYN1" "NBDY" "SIGIRR" "SMIM37" "STK17B"
## $immune
## category
## 4673 gse7548 naive vs day7 pcc immunization cd4 tcell dn
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 4673 9.748277e-06 0.9999995 6 65
## FDR
## 4673 0.0497747
##
## [1] "set_25"
## [1] "CD38" "IGLV2-14" "KIAA1328" "MBNL2" "RPS26" "SIMC1"
## [7] "XIST" "APOL1" "CCL5" "CCR4" "GZMA" "LINC01871"
## [13] "MYO1G" "RAP1GAP2" "RSAD2" "SAMD9L" "SPON2" "TGFBR3"
## [19] "VCAN"
## $immune
## category over_represented_pvalue
## 3623 gse3982 cent memory cd4 tcell vs nkcell dn 4.156056e-06
## under_represented_pvalue numDEInCat numInCat FDR
## 3623 0.9999999 5 35 0.02122082
##
## [1] "set_28"
## [1] "CD28" "KLF10" "ODC1" "SH3YL1" "AGAP2" "AP3M2" "AREG"
## [8] "CRIP2" "CRTC3" "EDA" "GABPB2" "ICOS" "IL21R" "KHNYN"
## [15] "LTBP3" "LY96" "NFKBIZ" "PLEKHA2" "SMAD5" "TOB1" "ZNF101"
## $reactome
## category over_represented_pvalue
## 174 constitutive signaling by aberrant pi3k in cancer 5.070047e-05
## under_represented_pvalue numDEInCat numInCat FDR
## 174 0.9999995 3 8 0.06089126
##
## [1] "set_35"
## [1] "ODF2L" "UTP6" "YPEL5" "ANKAR" "DTX3L" "FAM53B" "GBP1" "GBP3"
## [9] "GBP5" "GNLY" "HSH2D" "IFI44L" "IRF1" "IRF9" "MX1" "MYO1F"
## [17] "NKG7" "PARP14" "PARP9" "XAF1"
## $reactome
## category over_represented_pvalue under_represented_pvalue
## 478 interferon signaling 8.827006e-06 0.9999995
## 477 interferon gamma signaling 1.475343e-05 0.9999995
## numDEInCat numInCat FDR
## 478 7 88 0.008859437
## 477 5 35 0.008859437
##
## $go_bp
## category
## 623 defense response to symbiont
## 486 cellular response to type ii interferon
## 4273 response to type ii interferon
## 693 disruption of anatomical structure in another organism
## 4279 response to virus
## 4683 type ii interferon mediated signaling pathway
## 370 cell killing
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 623 3.728908e-08 1.0000000 9 81
## 486 1.089531e-07 1.0000000 6 25
## 4273 3.544879e-07 1.0000000 6 30
## 693 5.204098e-07 1.0000000 5 17
## 4279 5.741523e-07 1.0000000 9 110
## 4683 6.044950e-05 0.9999993 3 8
## 370 7.374768e-05 0.9999961 5 44
## FDR
## 623 0.0001783537
## 486 0.0002605613
## 4273 0.0005492341
## 693 0.0005492341
## 4279 0.0005492341
## 4683 0.0481883286
## 370 0.0503907347
##
## $immune
## category
## 4082 gse42724 naive bcell vs plasmablast up
## 473 gse14000 unstim vs 4h lps dc dn
## 1353 gse18791 unstim vs newcatsle virus dc 6h dn
## 4971 howard pbmc inact monov influenza a indonesia 05 2005 h5n1 age 19 39yo as03 adjuv
## 1456 gse19888 adenosine a3r inh vs act with inhibitor pretreatment in mast cell up
## 2348 gse26030 th1 vs th17 day5 post polarization up
## 4961 howard dendritic cell inact monov influenza a indonesia 05 2005 h5n1 age 18 49yo
## 4965 howard neutrophil inact monov influenza a indonesia 05 2005 h5n1 age 18 49yo 1dy
## 4972 howard t cell inact monov influenza a indonesia 05 2005 h5n1 age 18 49yo 1dy up
## 1343 gse18791 ctrl vs newcastle virus dc 8h dn
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 4082 0.000000e+00 1 11 67
## 473 6.436927e-11 1 10 62
## 1353 1.664468e-10 1 10 67
## 4971 1.739134e-10 1 10 67
## 1456 2.877583e-10 1 9 49
## 2348 5.031712e-10 1 9 52
## 4961 7.522654e-10 1 9 54
## 4965 7.926391e-10 1 11 104
## 4972 9.454219e-10 1 7 23
## 1343 2.348254e-09 1 9 61
## FDR
## 4082 0.000000e+00
## 473 1.643348e-07
## 1353 2.220005e-07
## 4971 2.220005e-07
## 1456 2.938588e-07
## 2348 4.281987e-07
## 4961 5.059019e-07
## 4965 5.059019e-07
## 4972 5.363694e-07
## 1343 1.199018e-06
##
## [1] "set_39"
## [1] "ABCC10" "ADGRG1" "AKNA" "CCL4" "CD300A" "CTSW"
## [7] "FCRL6" "FGFBP2" "GPR65" "MIAT" "PAXX" "RASAL3"
## [13] "S1PR5" "TRANK1" "TRAV29DV5" "TRBV12-3" "TSPAN32" "TTC38"
## [19] "USP30-AS1" "ZNF683"
## $immune
## category
## 4251 gse45739 unstim vs acd3 acd28 stim nras ko cd4 tcell dn
## 1623 gse21063 wt vs nfatc1 ko 16h anti igm stim bcell dn
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 4251 1.393901e-06 1.0000000 6 41
## 1623 1.408540e-05 0.9999997 4 17
## FDR
## 4251 0.007117258
## 1623 0.035960021
## used (Mb) gc trigger (Mb) limit (Mb) max used (Mb)
## Ncells 8958373 478.5 16391124 875.4 NA 16391124 875.4
## Vcells 19172611 146.3 57790505 441.0 65536 77218972 589.2
## R version 4.2.3 (2023-03-15)
## Platform: aarch64-apple-darwin20 (64-bit)
## Running under: macOS Ventura 13.4.1
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib
##
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## attached base packages:
## [1] stats4 stats graphics grDevices utils datasets methods
## [8] base
##
## other attached packages:
## [1] TxDb.Hsapiens.UCSC.hg38.knownGene_3.16.0
## [2] GenomicFeatures_1.50.4
## [3] GenomicRanges_1.50.2
## [4] GenomeInfoDb_1.34.9
## [5] org.Hs.eg.db_3.16.0
## [6] AnnotationDbi_1.60.2
## [7] IRanges_2.32.0
## [8] S4Vectors_0.36.2
## [9] Biobase_2.58.0
## [10] BiocGenerics_0.44.0
## [11] goseq_1.50.0
## [12] geneLenDataBase_1.34.0
## [13] BiasedUrn_2.0.10
## [14] fgsea_1.24.0
## [15] biomaRt_2.54.1
## [16] limma_3.54.2
## [17] tidyr_1.3.0
## [18] ggpubr_0.6.0
## [19] ggplot2_3.4.2
## [20] data.table_1.14.8
##
## loaded via a namespace (and not attached):
## [1] nlme_3.1-162 matrixStats_1.0.0
## [3] bitops_1.0-7 bit64_4.0.5
## [5] filelock_1.0.2 progress_1.2.2
## [7] httr_1.4.6 tools_4.2.3
## [9] backports_1.4.1 bslib_0.4.2
## [11] utf8_1.2.3 R6_2.5.1
## [13] mgcv_1.8-42 DBI_1.1.3
## [15] colorspace_2.1-0 withr_2.5.0
## [17] tidyselect_1.2.0 prettyunits_1.1.1
## [19] bit_4.0.5 curl_5.0.1
## [21] compiler_4.2.3 cli_3.6.1
## [23] xml2_1.3.4 DelayedArray_0.24.0
## [25] rtracklayer_1.58.0 sass_0.4.5
## [27] scales_1.2.1 rappdirs_0.3.3
## [29] Rsamtools_2.14.0 stringr_1.5.0
## [31] digest_0.6.31 rmarkdown_2.21
## [33] XVector_0.38.0 pkgconfig_2.0.3
## [35] htmltools_0.5.5 MatrixGenerics_1.10.0
## [37] dbplyr_2.3.2 fastmap_1.1.1
## [39] rlang_1.1.0 rstudioapi_0.14
## [41] RSQLite_2.3.1 BiocIO_1.8.0
## [43] jquerylib_0.1.4 generics_0.1.3
## [45] jsonlite_1.8.4 BiocParallel_1.32.6
## [47] dplyr_1.1.2 car_3.1-2
## [49] RCurl_1.98-1.12 magrittr_2.0.3
## [51] GO.db_3.16.0 GenomeInfoDbData_1.2.9
## [53] Matrix_1.6-4 Rcpp_1.0.10
## [55] munsell_0.5.0 fansi_1.0.4
## [57] abind_1.4-5 lifecycle_1.0.3
## [59] stringi_1.7.12 yaml_2.3.7
## [61] carData_3.0-5 SummarizedExperiment_1.28.0
## [63] zlibbioc_1.44.0 BiocFileCache_2.6.1
## [65] grid_4.2.3 blob_1.2.4
## [67] parallel_4.2.3 crayon_1.5.2
## [69] lattice_0.20-45 splines_4.2.3
## [71] Biostrings_2.66.0 cowplot_1.1.1
## [73] hms_1.1.3 KEGGREST_1.38.0
## [75] knitr_1.44 pillar_1.9.0
## [77] rjson_0.2.21 ggsignif_0.6.4
## [79] codetools_0.2-19 fastmatch_1.1-3
## [81] XML_3.99-0.14 glue_1.6.2
## [83] evaluate_0.20 png_0.1-8
## [85] vctrs_0.6.2 gtable_0.3.3
## [87] purrr_1.0.1 cachem_1.0.7
## [89] xfun_0.39 broom_1.0.4
## [91] restfulr_0.0.15 rstatix_0.7.2
## [93] tibble_3.2.1 GenomicAlignments_1.34.1
## [95] memoise_2.0.1